9 Biomarkers That Indicate Poor Gut Health

Discover the 9 key biomarkers that signal poor gut health and learn how to identify and improve your digestive wellness. Read our expert tips now!

9 Biomarkers That Indicate Poor Gut Health

Gut health biomarkers give objective clues about how your digestive system and microbiome are functioning. This article explains what these biomarkers are, why they matter, and how they relate to common symptoms like bloating, fatigue, or food sensitivities. You’ll learn about nine key indicators associated with inflammation, gut permeability, microbial balance, and toxin handling, along with the role of microbiome testing in providing personalized insight. Because symptoms can be misleading, understanding gut health biomarkers helps you move from guesswork to an informed, data-driven approach to digestive wellness.

Introduction

Interest in digestive wellness has expanded beyond traditional gastrointestinal disorders to include the gut microbiome—an ecosystem of bacteria, archaea, fungi, and viruses that interacts with your immune, nervous, and metabolic systems. As research grows, so does the recognition that gut health biomarkers can translate complex biology into measurable indicators. These biomarkers help us understand inflammation, gut barrier function, microbial balance, and metabolic byproducts that may influence well-being. While no single marker can “diagnose” the root cause of symptoms, a thoughtful combination of markers can sharpen the picture. This guide reviews nine widely discussed biomarkers, their significance, and how they fit into a responsible, personalized strategy for digestive health.

Core Explanation of the Topic

What Are Gut Health Biomarkers?

Biomarkers are measurable biological signals—molecules, metabolites, immune proteins, or physiological readouts—that provide information about body function or disease risk. In the context of gut health, biomarkers capture different aspects of digestive and microbial physiology. They can reflect intestinal inflammation, gut permeability (barrier function), microbial composition and diversity, fermentation balance, and exposure to microbial products (such as endotoxins). Biomarkers may be assessed through stool, blood, urine, or breath testing. While some, like fecal calprotectin, are used clinically as intestinal inflammation markers, others are emerging research tools that can guide preventive and personalized strategies.

The Significance of Monitoring Gut Health

The gastrointestinal tract is a dynamic interface between you and the external world. It helps digest and absorb nutrients, educates the immune system, and maintains a finely tuned barrier that allows beneficial compounds in while keeping potentially harmful particles out. When this system becomes imbalanced—through infections, stress, poor sleep, dietary extremes, medications, or other factors—biomarkers can shift in ways that point to inflammation, dysbiosis (microbial imbalance), or disrupted barrier integrity. Monitoring relevant biomarkers over time enables early detection of issues that might otherwise progress silently, supports decision-making about when to seek further evaluation, and helps evaluate whether nutrition, lifestyle, or clinical interventions are moving physiology in the right direction.

Why This Topic Matters for Gut Health

Digestive complaints are common, and many people experience intermittent bloating, irregularity, reflux, or food sensitivities. Meanwhile, research links the gut microbiome to immune regulation, cardiometabolic health, skin clarity, and even mood and cognition. Subtle changes in microbial communities or barrier function can influence systemic inflammation and immune activation. Left unaddressed, these imbalances may contribute to secondary problems—from nutrient malabsorption to chronic low-grade inflammation—especially in those with genetic predispositions or high allostatic load (the cumulative burden of stressors). Understanding and tracking gut health biomarkers can be part of a proactive, evidence-aware approach that looks beyond symptom management and toward the underlying biology.

Related Symptoms, Signals, or Health Implications

Common Symptoms That May Indicate Gut Dysfunctions

  • Bloating, gas, abdominal discomfort, altered bowel habits (constipation, diarrhea, or alternating patterns)
  • Unexplained fatigue, malaise, or “post-meal slump”
  • Frequent food sensitivities or difficulty tolerating high-FODMAP foods
  • Mood changes, irritability, low motivation, or cognitive fog
  • Skin issues such as acne, eczema, or rosacea that fluctuate with diet or stress

These symptoms are nonspecific. They can reflect benign, transient changes, but when persistent, they may warrant deeper exploration through history, examination, and judicious biomarker testing.


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Underlying Health Concerns

  • Chronic inflammation that can amplify pain and fatigue
  • Functional gastrointestinal disorders (e.g., IBS) or inflammatory conditions (e.g., IBD) that require medical oversight
  • Nutrient malabsorption (e.g., iron, B12, fat-soluble vitamins) contributing to fatigue or skin and hair changes
  • Immune dysregulation or heightened reactivity to foods or environmental antigens

Notably, a similar symptom pattern can arise from very different mechanisms. For example, both small intestinal bacterial overgrowth (SIBO) and pancreatic insufficiency can cause bloating, but the interventions and monitoring differ. That’s where objective digestive health indicators may help differentiate the picture.

Individual Variability and Uncertainty

Gut health is highly individualized. Two people can have the same biomarker value yet experience different symptoms—or none at all—because context matters: diet, medications, stress, sleep, exercise, environmental exposures, and genetics all shape how the gut and immune system behave. Even the same person may see biomarkers fluctuate across seasons, life stages, or after travel and illness. Many markers also exist on a physiological spectrum rather than a binary “good” or “bad,” and lab methods vary in how they collect and interpret data. Responsible interpretation acknowledges uncertainty, looks for patterns rather than relying on one number, and situates results within the person’s clinical picture.

Why Symptoms Alone Do Not Reveal the Root Cause

Relying solely on symptoms to infer what’s happening in the gut can be misleading. Bloating, for instance, might stem from rapid fermentation of carbohydrates in the small intestine (suggesting SIBO), slowed gut motility, stress-induced aerophagia (swallowing air), or food intolerance. Similarly, fatigue can reflect poor sleep, anemia, thyroid issues, depression, or chronic inflammation. Without objective testing, it’s easy to chase one theory after another and miss the real drivers. Biomarkers help validate or refute hypotheses and provide a baseline for measuring change. They don’t replace clinical judgment, but they do reduce guesswork and increase the chance that your efforts target the right mechanisms.

The Role of the Gut Microbiome in Digestive and Overall Health

How Microbiome Composition Affects Biomarkers

Your microbiome helps digest fibers into short-chain fatty acids (SCFAs), regulates bile acids, produces vitamins, and communicates with immune and nervous systems. When commensal microbes are abundant and diverse, they tend to support healthy inflammation control and barrier function. When dysbiosis develops—through antibiotic exposure, low-fiber diets, recurrent infections, or chronic stress—biomarkers can shift: SCFAs may decline, low-grade inflammation can rise, and immune proteins in stool may drift from optimal ranges. In this way, microbial balance or imbalance is reflected by multiple digestive health indicators rather than a single readout.

How Microbiome Imbalances May Contribute

  • Overgrowth of opportunistic bacteria or archaea can increase gas production, distention, and discomfort.
  • Reduced diversity may weaken colonization resistance (your microbiome’s ability to fend off unwanted microbes).
  • Altered fermentation patterns can elevate compounds such as p-cresol or ammonia, which may irritate the mucosa or affect detoxification pathways.
  • Insufficient butyrate-producing bacteria may compromise epithelial energy supply and tight junction signaling, influencing barrier integrity.

The Impact on Gut Permeability and Toxin Levels

The intestinal barrier is like a selectively permeable security system. It allows digested nutrients across while helping to contain bacteria and larger antigens. Inflammation, poor sleep, certain medications (e.g., NSAIDs), alcohol, and dysbiosis can disrupt tight junctions, sometimes referred to as “leaky gut.” When barrier integrity is compromised, more bacterial products, such as lipopolysaccharide (LPS), may reach the immune system and contribute to systemic inflammation. Correspondingly, biomarkers related to permeability and microbial translocation (e.g., zonulin family peptides, lactulose–mannitol ratio, LBP, sCD14) can rise. In stool, metabolite profiles may show increased “putrefactive” compounds or shifts in SCFAs that hint at an imbalanced ecosystem and higher gastrointestinal toxin levels.

9 Biomarkers That Indicate Poor Gut Health

Below are nine commonly discussed biomarkers and profiles that, when interpreted with clinical context, may indicate impaired gut function or microbial imbalance. None of these measures is diagnostic in isolation; patterns across markers are more informative than any single value.


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1) Fecal Calprotectin (Intestinal Inflammation)

What it is: Calprotectin is a calcium-binding protein released by neutrophils. Elevated levels in stool are a well-established marker of intestinal inflammation. Clinically, fecal calprotectin helps differentiate inflammatory bowel disease (IBD) from functional disorders like IBS, where calprotectin is typically normal.

How it’s measured: A stool test quantifies calprotectin, usually reported as micrograms per gram. Moderate elevations may warrant repeat testing or additional evaluation; persistently high levels generally prompt medical assessment to rule out IBD or other inflammatory conditions.

How to interpret: High calprotectin suggests active mucosal inflammation but does not specify the cause. Infections, NSAID use, and gastrointestinal bleeding can also elevate it. It’s a sensitive intestinal inflammation marker but must be paired with history, exam, and, when indicated, endoscopic evaluation.

2) Fecal Lactoferrin (Neutrophil-Derived Inflammation)

What it is: Lactoferrin is an iron-binding glycoprotein found in neutrophils. Similar to calprotectin, fecal lactoferrin rises with intestinal inflammation. It is helpful in distinguishing inflammatory conditions from functional ones and may track with disease activity in IBD.

How it’s measured: A stool immunoassay reports lactoferrin qualitatively or quantitatively. Persistently elevated results typically prompt further evaluation, especially when accompanied by alarm symptoms or systemic signs.

How to interpret: High lactoferrin supports an inflammatory process but, like calprotectin, is nonspecific regarding etiology. Combining both markers can improve confidence when screening for active mucosal inflammation.

3) Zonulin Family Peptides (Gut Barrier Regulation)

What it is: Zonulin modulates tight junctions between intestinal cells, influencing permeability. Elevated circulating or fecal zonulin-family peptides have been proposed as indicators of increased gut permeability. However, assay specificity and clinical interpretation remain areas of ongoing research.

How it’s measured: Blood or stool tests report zonulin or related peptides. Variability among assays and pre-analytical factors can affect results.

How to interpret: Higher values may suggest altered barrier function, but results should be viewed cautiously and corroborated with clinical context or additional gut permeability tests. Changes over time (in combination with symptoms and other biomarkers) may be more informative than a single measurement.

4) Lactulose–Mannitol Urinary Ratio (Functional Permeability Test)

What it is: This noninvasive test assesses how readily two sugar molecules pass through the small intestine. Mannitol is typically absorbed more easily than lactulose. When the intestinal barrier is compromised, larger amounts of lactulose can cross, raising the lactulose-to-mannitol (L/M) ratio.

How it’s measured: After ingestion of a standardized lactulose–mannitol solution, urine is collected over a specified period, and the excreted sugars are quantified. A higher L/M ratio suggests increased small-intestinal permeability.

How to interpret: An elevated L/M ratio may reflect a “leakier” barrier, though factors such as motility, renal function, and timing can influence results. It’s most useful when interpreted alongside symptoms and other biomarkers of inflammation or dysbiosis.

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5) Fecal Secretory IgA (Mucosal Immune Activity)

What it is: Secretory immunoglobulin A (sIgA) coats the mucosal surface, helping neutralize antigens and shape microbial communities. It represents frontline immune activity in the gut.

How it’s measured: Stool testing reports sIgA concentrations. Values can be low, normal, or elevated.

How to interpret: Low sIgA may indicate reduced mucosal immune “surveillance,” sometimes observed with chronic stress, undernutrition, or prolonged dysbiosis. High sIgA can reflect increased antigenic stimulation from infections, food antigens, or dysbiosis. Both low and high values are signals to investigate context, not standalone diagnoses.

6) Short-Chain Fatty Acids (SCFAs) and Butyrate Levels

What it is: SCFAs—primarily acetate, propionate, and butyrate—are microbial fermentation products of dietary fibers and resistant starch. Butyrate, the main fuel for colonocytes, supports barrier integrity, anti-inflammatory signaling, and colonic motility.

How it’s measured: Comprehensive stool analyses can quantify SCFAs, and some include additional metabolites such as branched-chain fatty acids or phenolic compounds.

How to interpret: Low total SCFAs—or specifically low butyrate—may suggest insufficient fiber intake, reduced butyrate-producing bacteria, or altered fermentation patterns. Disproportionately high branched-chain fatty acids or phenolic metabolites (e.g., p-cresol) can point toward protein putrefaction or an imbalanced microbial ecosystem. SCFA patterns are not disease-specific but can indicate whether the gut environment favors resilience or irritation.

7) Hydrogen and Methane on Breath Testing (SIBO-Related Gases)

What it is: Breath tests measure hydrogen and methane produced when bacteria ferment administered substrates (commonly lactulose or glucose). Elevated or early-peaking gases can suggest small intestinal bacterial overgrowth (SIBO) or intestinal methanogen overgrowth (IMO), both linked to bloating and altered motility.

How it’s measured: After ingesting a test sugar, breath samples are collected at intervals. Gas levels are plotted over time, and interpretation follows standardized criteria. Preparation protocols affect reliability.

How to interpret: Increased hydrogen typically aligns with carbohydrate-fermenting overgrowth; elevated methane is often associated with constipation and slower transit. Breath testing is an indirect indicator and should be considered alongside symptoms and other markers, as false positives and negatives can occur.

8) LPS-Related Markers: LBP and sCD14 (Microbial Translocation Signals)

What it is: Lipopolysaccharide (LPS) is a component of gram-negative bacterial cell walls. When LPS crosses a compromised intestinal barrier, the immune system responds. Lipopolysaccharide-binding protein (LBP) and soluble CD14 (sCD14) are blood markers that can rise with exposure to LPS, reflecting innate immune activation.

How it’s measured: Blood tests quantify LBP and sCD14. These are research-linked indicators used in some clinical contexts to assess immune response to microbial products.

How to interpret: Elevated LBP or sCD14 may suggest increased exposure to bacterial endotoxins. However, they are not specific to the gut, can be influenced by systemic infections or metabolic conditions, and should be interpreted cautiously and in context with other gut permeability tests or inflammatory markers.


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9) Microbial Diversity and Keystone Species (Community Resilience)

What it is: Alpha diversity metrics (e.g., Shannon index) estimate the richness and evenness of gut microbial communities. Presence of keystone taxa—such as select butyrate-producing Firmicutes or Akkermansia muciniphila—can indicate functional resilience. Low diversity has been associated, in research settings, with various chronic conditions.

How it’s measured: Microbiome profiling (e.g., 16S rRNA gene sequencing, shotgun metagenomics) provides taxonomic and sometimes functional information, from which diversity indices and relative abundances are derived.

How to interpret: Low diversity and reduced beneficial species may signal lower ecosystem stability and an increased likelihood of microbiome imbalance signs. Diversity is not a diagnosis, and “optimal” composition varies by person and diet. Still, consistently low diversity combined with symptoms and other abnormal biomarkers can strengthen the rationale for targeted dietary and lifestyle changes.

How Gut Microbiome Testing Provides Insight

What a Microbiome Test Can Reveal

Microbiome analysis offers a snapshot of which organisms are present and, in some cases, what functions they may perform. A well-constructed report can describe diversity, relative abundances of beneficial and opportunistic taxa, and potential functional capacities (e.g., SCFA production pathways, bile acid transformation). When combined with clinical biomarkers such as calprotectin, sIgA, or breath test results, microbiome data can clarify whether symptoms likely stem from fermentation patterns, barrier stress, or immune activation. For a closer look at what a structured report might include, see a microbiome test overview here: learn what a comprehensive microbiome test can show.

Additional Testing for Comprehensive Assessment

  • Gut permeability tests: Zonulin-family peptides and the lactulose–mannitol ratio can provide complementary views of barrier function.
  • Inflammatory markers: Fecal calprotectin and lactoferrin for intestinal inflammation; C-reactive protein (CRP) in blood for systemic inflammation.
  • Intestinal inflammation markers: Repeat testing can help track trends, especially when adjusting diet or medication.
  • Gastrointestinal toxin levels: While there is no single “toxin test,” stool metabolomics (e.g., p-cresol, ammonia) and LPS-related blood markers (LBP, sCD14) can suggest increased exposure to irritants or microbial products.

Testing should be tailored to the individual. In some cases, a focused panel is sufficient; in others, a staged approach—beginning with foundational markers and adding others if needed—can be more efficient and informative. If you are deciding whether to explore your microbial profile, this resource can help frame expectations: explore microbiome testing options and insights.

Who Should Consider Microbiome and Biomarker Testing

  • People with persistent digestive symptoms (bloating, irregularity, abdominal pain) not explained by routine evaluation
  • Individuals with autoimmune or chronic inflammatory conditions who want to assess whether gut factors might be contributing
  • Those experiencing fatigue, skin issues, or mood changes that seem linked to diet or digestion
  • Anyone seeking a personalized, data-informed plan for digestive wellness rather than relying on trial-and-error

Not everyone needs testing. If symptoms are mild and infrequent, foundational habits (fiber-rich diet, consistent sleep, stress management) may suffice. Testing makes more sense when symptoms are persistent, quality of life is affected, or simple adjustments have not led to meaningful improvement.

Decision-Support: When Does Testing Make Sense?

Indicators That Microbiome Testing Is Recommended

  • Ongoing or worsening digestive symptoms despite basic dietary and lifestyle changes
  • Multiple food sensitivities or unpredictable reactions without a clear pattern
  • History of recurring infections, frequent antibiotic use, or significant travel-related illness
  • Evidence or suspicion of systemic inflammation (e.g., elevated CRP) without an obvious cause
  • A desire to move beyond guesswork and tailor dietary fiber types, fermented foods, and other strategies to your biology

When several of these apply, a structured assessment can reduce uncertainty. If you are considering a home-based profile to better understand your microbiome’s composition and diversity, you can review an example offering here: at-home gut microbiome analysis.

How to Approach Testing and Interpretation

  • Work with a qualified clinician when possible. They can combine results with your history, medications, and physical findings.
  • Understand test limitations. No panel captures every nuance, and some markers (e.g., zonulin) have interpretive caveats.
  • Look for patterns over time rather than fixating on one-off values. Retesting after meaningful changes can help confirm directionality.
  • Use results to inform practical steps: adjust fiber types and amounts, diversify plant foods, evaluate FODMAP tolerance, consider probiotic or prebiotic strategies judiciously, and support sleep and stress regulation.

Practical Perspectives on Each Biomarker

It can be tempting to chase individual numbers, but a matrix view is more helpful. For instance, high fecal calprotectin with elevated lactoferrin strongly suggests active inflammation and warrants clinical oversight. A normal calprotectin with high breath methane and constipation might nudge attention toward motility and methanogen overgrowth. Low butyrate with low diversity and low sIgA could prioritize gradual fiber diversification, stress management, and immune support. Elevated LBP or sCD14 may push the focus toward barrier integrity, sleep, and systemic inflammation management while checking for other contributing factors. Tailoring intervention starts with a clear hypothesis informed by multiple, converging data points.

Why Symptoms and Single Tests Can Mislead

Symptoms can reflect many overlapping processes, and single tests capture only one perspective. A person may show normal calprotectin yet still feel unwell from rapid fermentation in the small intestine; conversely, a modestly elevated calprotectin might be transient after an infection and self-resolve. Breath testing can produce false positives if preparation is not followed or if rapid transit alters timing. Microbiome diversity can be temporarily lowered after antibiotics yet rebound with time and diet. This is why longitudinal assessment—retaking relevant tests after meaningful changes—is often more revealing than a single snapshot.

Building a Personalized Gut Health Plan

Using biomarkers responsibly means aligning them with your goals and tolerances. If gas and bloating are primary complaints, you might prioritize breath testing, stool SCFAs, and a microbiome profile to guide fermentable fiber strategies. If fatigue and inflammatory symptoms dominate, pairing calprotectin with CRP and, in select cases, LBP or sCD14 may be reasonable. For frequent food reactions, sIgA can contextualize immune activity, and a gut permeability test may be informative. Once results are in hand, simple, sustainable actions—appropriate fiber and protein balance, diverse plant intake, prudent use of fermented foods, consistent sleep, and stress regulation—often move multiple biomarkers in a favorable direction.

Key Takeaways

  • Gut health biomarkers translate complex gut and microbiome biology into measurable signals.
  • No single marker diagnoses root cause; patterns across inflammation, permeability, and microbiome data are most informative.
  • Calprotectin and lactoferrin are established intestinal inflammation markers useful in clinical triage.
  • Zonulin-family peptides and the lactulose–mannitol ratio can suggest altered gut permeability but require careful interpretation.
  • SCFAs, breath gases, and microbial diversity reflect fermentation balance and ecosystem resilience.
  • LPS-related markers (LBP, sCD14) may signal microbial translocation but are not gut-specific.
  • Symptoms alone often mislead; objective testing reduces guesswork and supports targeted strategies.
  • Results should be interpreted with clinical context and, when possible, with guidance from a qualified practitioner.

Frequently Asked Questions

Are gut health biomarkers diagnostic on their own?

No. Biomarkers are informative but not definitive diagnoses. They help identify patterns—such as inflammation or dysbiosis—that guide further evaluation and personalized strategies when combined with history, examination, and clinical judgment.

How reliable are tests like zonulin for gut permeability?

Zonulin-family assays are promising but still debated regarding specificity and standardization. They can be used as part of a broader assessment, ideally alongside symptoms and other permeability indicators such as the lactulose–mannitol ratio.

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What’s the difference between IBS and IBD in terms of biomarkers?

IBS is a functional disorder often showing normal calprotectin and lactoferrin, while IBD is inflammatory and typically elevates these markers. However, overlaps and exceptions exist, so clinical evaluation remains essential.

Can dietary changes significantly alter biomarkers?

Yes. Increased fiber diversity can raise butyrate and total SCFAs, while excessive alcohol or NSAID use may worsen permeability and inflammation. Diet, sleep, stress, and activity commonly influence biomarker trajectories over weeks to months.

Do probiotics normalize gut biomarkers?

Some probiotic strains have evidence for specific outcomes (e.g., reducing antibiotic-associated diarrhea), but effects are strain- and context-dependent. Probiotics are not a cure-all; diet quality, fiber diversity, and lifestyle often have broader impacts on microbiome function.

How often should I retest?

It depends on goals and symptom changes. For many, retesting relevant markers after 8–12 weeks of meaningful dietary or lifestyle adjustments can reveal trends. For clinical conditions (e.g., IBD), follow clinician guidance for monitoring intervals.

Is low microbial diversity always a problem?

Low diversity is associated with reduced resilience in many studies, but context matters. Temporary reductions after antibiotics or illness may recover with time and diet, and diversity “targets” vary by population and dietary pattern.

What breath test should I choose—glucose or lactulose?

Glucose breath tests are more specific for proximal small intestine overgrowth, while lactulose can assess distal segments but may be more prone to false positives from rapid transit. Choice depends on clinical suspicion and practitioner preference.

Can stress alone affect gut biomarkers?

Chronic stress can alter motility, increase intestinal permeability, and modulate immune activity, potentially shifting markers like sIgA or permeability indicators. Sleep quality and stress management often improve both symptoms and biomarker profiles.

Are LBP and sCD14 specific to gut-derived inflammation?

No. They reflect immune activation in response to LPS, which can enter circulation from the gut but also from other sources. Elevated values require careful interpretation and correlation with gastrointestinal and systemic findings.

Do I need a microbiome test if I feel fine?

Not necessarily. If you’re asymptomatic and following balanced habits, testing may not add actionable information. It becomes more valuable when symptoms persist, recur, or you want to personalize nutrition beyond general guidelines.

Where does a home microbiome test fit in my workup?

It can complement clinical markers by illuminating composition, diversity, and functional potential. If you’re exploring a data-informed approach to diet and lifestyle, reviewing an example offering like this home microbiome assessment can help set expectations.

Conclusion

Understanding gut health biomarkers equips you to move from symptom guessing to informed exploration. Markers of inflammation (calprotectin, lactoferrin), permeability (zonulin-family peptides, lactulose–mannitol ratio), microbial balance (diversity, SCFAs), SIBO-related gases (hydrogen, methane), and immune response to microbial products (LBP, sCD14) together help map the terrain. Because biology is individualized, interpretation should be cautious, contextual, and, when possible, clinician-guided. If you want deeper, personalized insight into your microbiome’s composition and resilience, reviewing a structured testing option—such as this overview of gut microbiome testing—can be a thoughtful next step toward long-term digestive wellness.

Keywords

gut health biomarkers, intestinal inflammation markers, digestive health indicators, microbiome imbalance signs, gut permeability tests, gastrointestinal toxin levels, fecal calprotectin, fecal lactoferrin, zonulin, lactulose–mannitol test, secretory IgA, SCFAs, butyrate, hydrogen methane breath test, LPS, LBP, sCD14, microbial diversity, dysbiosis, personalized gut health, microbiome testing

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